Lenski experiment and falsifiability

Faith & Science Conversation
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There is a difference between proving evolution and failing to falsify evolution. If you found a fossil record that was wildly out of sync with evolution’s predictions, evidence the earth was young, or organisms who did not have DNA or whose DNA was wildly different from similar organisms, that would indeed falsify evolution. So far none of these things have been found. The absence of these things doesn’t prove evolution, it just means it’s a good model consistent with evidence. What ID should be doing instead of trying to falsify evolution is coming up with a viable design model that offers a better explanation. They have failed to do this, which is why evolution is the preferred model.

Sure. Here.

In the following list of evidences, 30 major predictions of the hypothesis of common descent are enumerated and discussed. Under each point is a demonstration of how the prediction fares against actual biological testing. Each point lists a few examples of evolutionary confirmations followed by potential falsifications.

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(Appreciated, But this link deals only with common descent, and specifically does not address the question of method. While I have my doubts about universal common descent, that isn’t my interest, rather, the ability to falsify the sufficiency of the variation/natural selection mechanism to account for biological complexity is my main question.)

From the linked page…

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Which is a good quote because with common descent established beyond reasonable doubt, it doesn’t actually matter what mechanisms lie behind the change. We can have confidence that it did indeed occur (and if it didn’t, the Designer made things look as if they all share common descent, even modern humans but that’s like saying God made a universe fully mature where he put the radioactive isotope ratios, globular cluster main sequence stars, and other astrophysical phenomenon with a false billion year history).

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So the mechanism could have been an intelligent agent?

I fear you are missing my point. Darwinian mechanism (variation & natural selection) is a distinct, albeit related, theory from the idea of universal common descent. While I have my doubts about universal common descent, I don’t particularly take significant issue with the idea either. Some common descent is clearly undeniable. It is the macro-evolutionary mechanism that I find unbelievable.

One could believe (like Behe and many others) in common descent of all life from a single initial ancestor for life, but that the blind Darwinian mechanism is simply insufficient to explain the vast increases in complexity, and that God’s or another designer’s involvement was necessary at numerous points along the history of life.

Simply put, if common descent could be established beyond a reasonable doubt, then sure, we have confidence that common descent occurred. This does not somehow prove that Darwinian evolution happened… i.e., the sufficiency of the variation/natural selection method.

I am asking if Darwinian macroevolution … specifically, the theory that the development development of increasingly (and stunningly) complex life is sufficiently explained solely by blind chance and random variation, as filtered through natural selection… is empirically falsifiable, and if so, how?

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Are you aware that a platypus bill and a bird beak have very different structures and only appear similar to each other?

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Sure, and presumably a rabbit discovered with feathers would not falsify evolution for similar reasons.

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But they aren’t … and they haven’t. Maybe you were just giving a quick flippant reply there, but if a Platypus was found that had a true bird beak or a rabbit was discovered with actual feathers, then that would fly in the face of existing theory.

It sounds to me like there is plenty of room left in existing evolutionary theory to leave open the question of the sufficiency of the traditionally accepted mechanisms - or what you call “Darwinian evolution”. I gather that our knowledge of evolution has evolved enough since Darwin’s time that to criticize it for being Darwinian would be a bit like attacking “Newtonian Gravity” on the grounds that Newton’s understandings didn’t include Einstein’s insights about space-time.

I for one join you in thinking that there is yet much to be explained about evolution and its mechanisms. Where many of us balk a bit is in letting those gaps be filled with the reflexive “…therefore God.” Because for most of us, to jump on that last conclusion is to implicitly concede that everything prior must therefore have been “not God”.

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Or a dolphin sharing the same genes as a bat. But no, the theory would simply adapt to incorporate one more striking example of “convergent evolution.”

From the article:

The researchers discovered genetic signatures consistent with convergence in nearly 200 genomic regions when it came to dolphins and echolocating bats. Many of these genes are linked with hearing or deafness. These similarities were not seen with non-echolocating animals.
We didn’t expect to see more than perhaps 10 to 30 genes converge, probably mainly hearing-related ones," researcher Joe Parker, an evolutionary biologist at Queen Mary University of London, told LiveScience. “Instead, we were able to detect many times that number.”
Unexpectedly, the researchers also found convergence in many genes linked to vision. This makes sense, given how bats and dolphins are typically active in dim lighting.
”Natural selection can be a very powerful force for shaping genetic sequences, and the outcomes of that process can be very similar, even in unrelated organisms," Parker said.

So bats and dolphins share features that are the same at a genetic level, not simply appearance of structural similarity. But no, this neither proves they were related, nor does it falsify common descent… It is merely a striking example of the power of convergent evolution, no one seems to take it as evidence with which to even consider falsifying the overall theory.

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Others more knowledgeable will have to speak to any genetic similarity these features have in common. To my layman’s ears, this doesn’t stretch any bounds of credibility for convergent evolution; I would compare it to a slightly more sophisticated version of unrelated animals developing flight.

There is indeed some elasticity of a good theory that has the scope that evolutionary theory has - but not infinite elasticity as some want to imagine. The theory is constrained by reality and it is easy to imagine many findings that (if confirmed and born out) would falsify the whole enterprise. Such scenarios have been shared here before.

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I would like to believe that, but the discussion on this thread thus far is confirming my suspicions that the theory is simply not falsifiable. If I lived a million years, observed every species remain essentially unchanged over that time, this would seem insufficient to falsify the theory. Just because they never changed while I was watching over countless generations, that is no evidence that the process didn’t previously work when I wasn’t watching, just like all the “living fossils” extant don’t disprove the theory.

It is reminiscent of that “super hero” in Mystery Men, that had the power to turn invisible… so long as no one was watching.

The only falsifying criteria that anyone has offered relates to falsifying common descent. And, while interesting, and certainly related, it is not my main question. Disproving common descent may indeed consequentially disprove evolutionary theory, but the converse is not true. Common descent can be true, while macroevolution via natural selection / variation could be untrue. I’m asking if there is any empiric, scientific means by which the standard naturalistic macroevolutionary theory could be disproved as a mechanism in itself, even if common descent were true.

Normally, one would try to repeat the conditions (if possible) to test the theory and demonstrate some level of repeatability, with certain results allowing falsifiability. I personally would be convinced of the process if we could observe organisms with short generation times (bacteria, protozoa, etc.) develop novel structures or functions from significant amounts of new novel code over comparable generations (comparable to the timeframe such novel information is purported to have appeared in other animals). In such a case, I’d say the theory was tested and confirmed,

However, if the process we can observe does not show this ability, even over comparable generations… even in lab settings, with lots of coaxing, or in nature with near limitless opportunities, why should I be asked to believe in the reality of a natural biological process without empiric evidence, a process which it seems is neither observable, repeatable, testable, nor falsifiable?

I’m afraid it seems to me that this particular theory does in fact have infinite elasticity.

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I’m not an expert in echolocation genetics, but it appears you are reading too much into the quote. Parker says the outcomes of the process can be very similar, not the actual gene sequences themselves. Genetic sequences can produce similar anatomical and physiological structures without having an equally matching level of DNA sequence similarity.

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I should probably also add, even though you and I cannot echolocate without serious risk of a broken nose, there are quite a few humans that have learned to refine the inherent ability.

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didn’t you answer your own question? These organisms or not out in the wild where we would expect more environmental niches to populate, resulting in a more diverse genetic makeup.

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Curtis, good to hear from you, great to interact with you as always!

My reading comprehension is either very, very, very poor, or they are in fact saying that the gene sequences themselves match… please feel free to fact-check me here, but I don’t think I’ve misread that badly…

“We had expected to find identical changes in maybe a dozen or so genes but to see nearly 200 is incredible," explains Dr. Joe Parker, first author on the paper. “We know natural selection is a potent driver of gene sequence evolution, but identifying so many examples where it produces nearly identical results in the genetic sequences of totally unrelated animals is astonishing.”

Bats and dolphins trod an identical genetic path to evolve a vital component of the complex sonar systems they use to pursue and catch prey.
The finding is unusual, because although many creatures have independently evolved characteristics such as eyes, tusks or wings, they usually took diverse genetic routes to get there.
Analysis of a specific gene has now demonstrated that although bats live in air and dolphins in water, where sound travels five times faster, they independently evolved a near-identical gene that allows them to accept high-frequency sound in the ear – vital for sonar.

https://www.sciencemag.org/news/2013/09/bats-and-dolphins-evolved-echolocation-same-way

Until recently, biologists had thought that different genes drove each instance of echolocation and that the relevant proteins could change in innumerable ways to take on new functions… But in 2010, Stephen Rossiter, an evolutionary biologist at Queen Mary, University of London, and his colleagues determined that both types of echolocating bats, as well as dolphins, had the same mutations in a particular protein… The analysis revealed that 200 genes had independently changed in the same ways.

Of course, I’m sure this is still far better explained by the amazing powers of natural selection, somehow orchestrating the astronomically ridiculous odds of seeing 200 genes mutate in near identical ways, rather than any conceivable alternative. :wink:

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Hi Daniel, good to talk with you, too!

Looks like you were absolutely right. I’ll do some actual reading over this, but it will probably be next week. Thanks for supplying the material!

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Boy, it does to me. Maybe just because I’m strange and I actually like to think about the math involved. So I crunched some of the numbers…

Natural selection can only work with the mutations given it by sheer dumb random luck. Even if natural selection in this case were perfectly honed, somehow focused on nothing but selecting the perfect mutations for echolocation, and thus guaranteed to reject any mutation except the very perfect ones that would make dolphin and bat genes match, those mutations still have to show up by random chance. The odds of that just by itself get ridiculously slim:

The odds of any particular point mutation happening at a particular base pair in mammals over one generation is like 1/220,000,000, but we only have around 1,000,000 generations or so to work with. This isn’t an obstacle for natural selection in general, as it can work with whatever it is given, and with all the genes involved, some mutations are likely to happen somewhere in the genome each generation, and natural selection can work with any such mutation(s) that confers any benefit.

But to get any particular mutation, that means there’s still only something like a 1/200 chance that the specific base will even experience a mutation in the time allotted, and even if it does, still only a fraction of that time will it will be the right base substituted. All that for just one mutation. And we’re talking 200 genes worth of mutations that all have to get just the right mutations to show up in just the right places. That by itself stretches credibility far past the breaking point.

But it is far worse than that… natural selection simply doesn’t exert that kind of specificity or teleology. It doesn’t know it is trying to match the bat genes to dolphin genes or develop a particular kind of echolocation. It isn’t going to presciently reject every mutation except those which happen to be identical to those mutations in another species, or which are needed for some particular feature, regardless of whatever “selective pressure” is exerted. It just doesn’t work that way. The different species will experience different mutations in those genes, and natural selection is going to accept any mutations which confer any benefit to the organism (and potentially any which are essentially neutral and do no damage).

It is simply inconceivable that (across 200(!) genes no less) either random chance could have provided these two organisms the exact same mutations, or that natural selection could have operated with the kind of near-magic specificity required to reject any mutation except those which happen to make them mirror those same mutations of a different species.

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If a critter has been able to exist for millions of years without evolving, then there is no evolutionary reason for it to evolve. The critter has no problem passing its DNA on to the next generation.

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You’re absolutely right! I don’t think I’ve heard any biologists around here describing evolution as working that way. I don’t know how teleology or intention could be ascribed to mechanical phenomena. It takes mind or will to have those things. That’s another amazing thing that I suspect is beyond science.

So you’ve crunched some numbers and found incredible odds. You sound like an engineer - but you’ll have to remind me of your profession or area of expertise - I’m guessing it isn’t in the life sciences; but at least you’re ahead of me if it is. That’s why I like to rely on the appraisals and applied knowledge of the experts in those areas. I know - they can be wrong or ideologically misguided too. But they are much less likely to have strayed than those of us speculating from outside their fields. So forgive me for not jumping away from mainstream consensus over a couple engineering-like computations that show the improbability of your version of how evolution is supposed to work.

Every part of a living body looks amazing to me, whether it be the “simple” hand or something as sophisticated as echolocation. That various creatures share some of these same kinds of general features (to help them navigate and survive in similar physical environments after all!) does not rise significantly higher over my already grateful surprise that our universe with life is here at all.

I think we agree that God is an amazing Creator. I hope to always work for a greater understanding for how this creation works, and so don’t want to foreclose on the “possible range of God’s activity” in ways that may prevent me from accepting God’s truth about creation. Or at least I don’t want to turn away from truth that we should reasonably be expected to handle.

Thanks for your continued conversation.

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I apologize in advance for the long quote, but you need to read the original paper to understand the methods and what can be concluded from them:

To detect genome-wide sequence convergence between echolocating lineages, we built an analytical pipeline based on maximum likelihood (ML) phylogenetic reconstruction8,10,19. In this method, we examined each amino acid along the alignment of a given CDS, and measured its fit (site-wise log-likelihood support; SSLS) to the commonly accepted species tree23,24,25(hereafter termed H0) and to two alternative topologies in which we forced echolocating taxa into erroneous monophyletic clades representing different convergence hypotheses (see Fig. 1a; for details see Supplementary Fig. 1 and Methods): H1 corresponds to all echolocating bats in a monophyletic group (‘bat–bat convergence’) and H2 to all echolocating mammals together in a monophyletic group (‘bat–dolphin convergence’). Using this approach we obtained the SSLS values of all amino acids under three different tree topologies. The difference in SSLS for a single site under the species tree and a given convergent tree with an identical substitution model denotes the relative support for the convergence hypothesis; for example, ΔSSLS (H1) = SSLS (H0) − SSLS (H1) (where negative ΔSSLS implies support for convergence; see Supplementary Fig. 2). We quantified the extent of sequence convergence at each locus by taking the mean of its ΔSSLS values, and found 824 loci with mean support for H1 and 392 for H2. Using simulations we confirmed that these convergent signals were not due to neutral processes and were robust to the substitution model used.

Long story short, the study provides strong evidence that separate genetic evolutionary pathways were taken to the same echolocation goal.

The original is free for all readers here.

P.S. Daniel, I really like your avatar. Have you served aboard a submarine?

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Just to clarify, do you mean different paths led to the identical mutations, or that the genes in question did not, in fact, have the same mutations

I’m not familiar enough with the intricacies myself, but I’d be curious why the scientists who actually did the research summarized it by saying…

“It means that high-frequency hearing fundamental to echolocation evolved through the same molecular route,” says Stephen Rossiter of Queen Mary, University of London.

And yes, I have spent a good amount of time in submarines. Great times.

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